# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 02:01:06 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: L-homocysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCS)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 HCS  HCS  'L-homocysteine           '  L-peptide  16  8  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HCS
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 HCS  N    N  NH2    0  -0.819  -32.7441  20.7526  -0.9528
 HCS  CA   C  CH1    0  -0.214  -32.9754  22.0069  -0.2509
 HCS  CB   C  CH2    0  -0.393  -31.6533  22.7362  -0.0075
 HCS  CG   C  CH2    0  -0.552  -30.6866  21.9034   0.8191
 HCS  SD   S  S2     0  -0.265  -29.1573  22.8643   1.0957
 HCS  C    C  C      0   0.413  -33.9761  22.9083  -1.0264
 HCS  OXT  O  OC    -1  -0.597  -34.6148  22.3743  -1.9554
 HCS  O    O  O      0  -0.603  -34.0785  24.0847  -0.6295
 HCS  H    H  HNH2   0   0.336  -33.5745  20.5475  -1.4939
 HCS  H2   H  HNH2   0   0.332  -32.6218  19.9947  -0.2953
 HCS  HCA  H  HCH1   0   0.199  -33.4378  21.8399   0.7373
 HCS  HB2  H  HCH2   0   0.214  -31.1925  22.9773  -0.9707
 HCS  HB3  H  HCH2   0   0.221  -31.8528  23.6793   0.5026
 HCS  HG2  H  HCH2   0   0.254  -31.1296  21.6486   1.7834
 HCS  HG3  H  HCH2   0   0.259  -30.4322  20.9787   0.3023
 HCS  HD   H  HSH1   0   0.216  -28.4638  21.9305   1.7565

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 HCS  N   CA   single  1.458  0.019  1.458
 HCS  N   H    single  0.860  0.020  0.860
 HCS  N   H2   single  0.890  0.020  1.040
 HCS  CA  CB   single  1.521  0.033  1.521
 HCS  CA  C    single  1.525  0.021  1.525
 HCS  CA  HCA  single  0.970  0.020  1.090
 HCS  CB  CG   single  1.520  0.020  1.520
 HCS  CB  HB2  single  0.970  0.020  1.090
 HCS  CB  HB3  single  0.970  0.020  1.090
 HCS  CG  SD   single  1.827  0.020  1.827
 HCS  CG  HG2  single  0.970  0.020  1.090
 HCS  CG  HG3  single  0.970  0.020  1.090
 HCS  SD  HD   single  1.200  0.020  1.300
 HCS  C   OXT  deloc   1.247  0.020  1.247
 HCS  C   O    deloc   1.231  0.020  1.231

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 HCS  H2   N   H    107.16  3.000
 HCS  H2   N   CA   110.59  3.000
 HCS  H    N   CA   114.00  3.000
 HCS  HCA  CA  C    105.35  3.000
 HCS  HCA  CA  CB   106.96  3.000
 HCS  C    CA  CB   110.50  1.500
 HCS  HCA  CA  N    111.58  3.000
 HCS  C    CA  N    111.00  2.800
 HCS  CB   CA  N    110.40  1.500
 HCS  HB3  CB  HB2  107.35  3.000
 HCS  HB3  CB  CG   109.62  3.000
 HCS  HB2  CB  CG   109.35  3.000
 HCS  HB3  CB  CA   109.19  3.000
 HCS  HB2  CB  CA   109.20  3.000
 HCS  CG   CB  CA   112.02  3.000
 HCS  HG3  CG  HG2  108.40  3.000
 HCS  HG3  CG  SD   108.83  3.000
 HCS  HG2  CG  SD   109.19  3.000
 HCS  HG3  CG  CB   110.83  3.000
 HCS  HG2  CG  CB   110.50  3.000
 HCS  SD   CG  CB   109.05  3.000
 HCS  HD   SD  CG    98.14  3.000
 HCS  O    C   OXT  126.83  3.000
 HCS  O    C   CA   120.80  1.700
 HCS  OXT  C   CA   120.80  1.700

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 HCS  Var_01  SD  CG  CB  CA  -178.59  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 HCS  chir_01  CA  N  CB  C  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 HCS  plan-1  CA   0.020
 HCS  plan-1  C    0.020
 HCS  plan-1  OXT  0.020
 HCS  plan-1  O    0.020

